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Plasmids are extrachromosomal DNA molecules found in bacteria, archaea, and some eukaryotic microbes like yeast. These small, circular DNA structures typically contain fewer than 30 genes, although some may exist linearly. Plasmids vary in their number within a cell, known as copy number. Single-copy plasmids are present in one copy per cell and multi-copy plasmids are present in multiple copies, reaching over 100 copies per cell.Plasmids usually replicate independently of the chromosomal DNA...
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Cell sizes vary widely among and within organisms. Bacterial cells range between 1-10 micrometers (μm)and are considerably smaller than most eukaryotic cells. The smallest bacteria are 0.1 μm in diameter—about a thousand times smaller than eukaryotic cells, which typically range from 10-100 μm.
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Enthalpy changes are typically tabulated for reactions in which both the reactants and products are at the same conditions. A standard state is a commonly accepted set of conditions used as a reference point for the determination of properties under other different conditions. For chemists, the IUPAC standard state refers to materials under a pressure of 1 bar and solutions at 1 M and does not specify a temperature. Many thermochemical tables list values with a standard state of 1 atm. Because...
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On comparing the reactivity of silver and lead, it is observed that the two ionic species, Ag+ (aq) and Pb2+ (aq), show a difference in their redox reactivity towards copper: the silver ion undergoes spontaneous reduction, while the lead ion does not. This relative redox activity can be easily quantified in electrochemical cells by a property called cell potential. This property is commonly known as cell voltage in electrochemistry, and it is a measure of the energy which accompanies the charge...
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The free energy change for a reaction that occurs under the standard conditions of 1 bar pressure and at 298 K is called the standard free energy change. Since free energy is a state function, its value depends only on the conditions of the initial and final states of the system. A convenient and common approach to the calculation of free energy changes for physical and chemical reactions is by use of widely available compilations of standard state thermodynamic data. One method involves the...
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Homemade Site Directed Mutagenesis of Whole Plasmids
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An improved plasmid size standard, 39R861.

Robert A Moran1, Sashindran Anantham1, Ruth M Hall1

  • 1School of Life and Environmental Sciences, The University of Sydney, NSW, Australia.

Plasmid
|February 11, 2019
PubMed
Summary

Accurate plasmid DNA size standards are crucial for molecular biology. This study precisely determined the sizes of key plasmids in E. coli 39R861 and developed an enhanced standard, 39R861+, for improved accuracy.

Keywords:
39R861ElectrophoresisPlasmid sizingStandard

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Area of Science:

  • Molecular Biology
  • Genomics
  • Microbiology

Background:

  • The E. coli 39R861 strain contains four plasmids historically used as size standards for closed-circular DNA.
  • Previous estimations of these plasmid sizes lacked precision, impacting their reliability in molecular biology applications.

Purpose of the Study:

  • To accurately determine the sizes of the plasmids within the E. coli 39R861 strain.
  • To develop an improved and more accurate plasmid size standard for molecular biology research.

Main Methods:

  • Whole-genome sequencing was employed to determine the complete sequence and size of the FII plasmid p39R861-3 (61.3 kb).
  • Plasmid sizes for p39R861-4, pSa, and NTP168 were precisely determined using sequencing data.
  • An enhanced plasmid size standard, 39R861+, was constructed by conjugating two additional sequenced, compatible plasmids into the original 39R861 strain.

Main Results:

  • The precise sizes determined were: p39R861-3 (61.3 kb), p39R861-4 (155.8 kb), pSa (40.1 kb), and NTP168 (6.8 kb).
  • The enhanced 39R861+ standard comprises six stably maintained plasmids, including the conjugative B/O plasmid p838B-R (94.8 kb) and the cryptic pBuzz (2.0 kb).

Conclusions:

  • The precise characterization of E. coli 39R861 plasmids provides accurate size references for closed-circular DNA.
  • The newly developed 39R861+ standard offers enhanced accuracy and reliability for molecular size determination in various applications.